skinnider
commented
1 year ago For this study, the DE results provided by the authors were used in lieu of re-doing the bulk DE ourselves, as the bulk RNA-seq from the study was not made publicly available - cf. the Methods section of our publication:
Reyfman et al., 201915. scRNA-seq data from the lungs of patients with pulmonary fibrosis and healthy controls was obtained from GEO (GSE122960). Metadata, including cell type annotations, was provided by the authors. One sample (“Cryobiopsy_01”) was removed as it was sequenced separately from the rest of the experiment. The results of DE analysis of bulk RNA-seq data, comparing purified AT2 cells or alveolar macrophages from patients with pulmonary fibrosis and healthy controls, were obtained from the supporting information accompanying the original publication. DE analysis was performed by comparing cells from patients with pulmonary fibrosis and controls.
AnthoOzier
Hello, I am trying to reproduce your analyses on the 18 'ground truth' datasets provided with your paper on Zenodo (https://doi.org/10.5281/zenodo.5048449) and I realized that the two bulk datasets "Reyfman2020_alvmac.rds" "Reyfman2020_pneumo.rds" do not contain the slots assay and meta but contain instead the test outputs columns "log2FoldChange", "lfcSE", "stat", "pvalue", "padj" ... Same thing in the directory matrices, instead of having the files "samples", "features", "matrix", "meta", we only have a file "results" for the Reyfman datasets.
Could you provide me the original bulk datasets and/or tell me which test have been run to obtain these outputs ?
Edit : I deduced from the column names that it was DEseq2.
Thank you in advance !